Trim Galore! is a wrapper script to automate quality and adapter trimming as well as quality control, with some added functionality to remove biased methylation positions for RRBS sequence files (for directional, non-directional (or paired-end) sequencing). It's main features are:

• For adapter trimming, Trim Galore! uses the first 13 bp of Illumina standard adapters ('AGATCGGAAGAGC') by default (suitable for both ends of paired-end libraries), but accepts other adapter sequence, too
• For MspI-digested RRBS libraries, Trim Galore! performs quality and adapter trimming in two subsequent steps. This allows it to remove 2 additional bases that contain a cytosine which was artificially introduced in the end-repair step during the library preparation
• For any kind of FastQ file other than MspI-digested RRBS, Trim Galore! can perform single-pass adapter- and quality trimming
• The Phred quality of basecalls and the stringency for adapter removal can be specified individually
• Trim Galore! can remove sequences if they become too short during the trimming process. For paired-end files Trim Galore! removes entire sequence pairs if one (or both) of the two reads became shorter than the set length cutoff. Reads of a read-pair that are longer than a given threshold but for which the partner read has become too short can optionally be written out to single-end files. This ensures that the information of a read pair is not lost entirely if only one read is of good quality
• Trim Galore! can trim paired-end files by 1 additional bp from the 3' end of all reads to avoid problems with invalid alignments with Bowtie 1
• Trim Galore! accepts and produces standard or gzip compressed FastQ files
• FastQC can be run on the resulting output files once trimming has completed (optional)

• http://www.bioinformatics.babraham.ac.uk/projects/trim_galore/

• Module Name: trimgalore (see the modules page for more information)
• Example files in /usr/local/apps/trimgalore/version/test_files

Allocate an interactive session and run the program. Sample session:

[user@biowulf]$ sinteractive
salloc.exe: Pending job allocation 46116226
salloc.exe: job 46116226 queued and waiting for resources
salloc.exe: job 46116226 has been allocated resources
salloc.exe: Granted job allocation 46116226
salloc.exe: Waiting for resource configuration
salloc.exe: Nodes cn3144 are ready for job

[user@cn3144 ~]$ module load trimgalore
[user@cn3144 ~]$ trim_galore inputfile

[user@cn3144 ~]$ exit
salloc.exe: Relinquishing job allocation 46116226
[user@biowulf ~]$

Create a batch input file (e.g. trimgalore.sh). For example:

#!/bin/bash
set -e
module load trimgalore
trim_galore inputfile [options...]

Submit this job using the Slurm sbatch command.

sbatch [--mem=#] trimgalore.sh

Create a swarmfile (e.g. trimgalore.swarm). For example:

cd dir1; trim_galore infile
cd dir2; trim_galore infile
cd dir3; trim_galore infile
cd dir4; trim_galore infile

Submit this job using the swarm command.

swarm -f TEMPLATE.swarm [-g #] --module trimgalore